Results are preliminary

Low precision for some parameters.

Primary author: Manon Ragonnet and Erik Volz

Report prepared on 2020-04-09 (updated April 20, 2020 )

Olivia Boyd, Lily Geidelberg, David Jorgensen, Manon Ragonnet, Igor Siveroni, Erik Volz and the Imperial College COVID-19 Response Team

Background information

This is analysis is based on :

  • 152 whole genomes sampled from within Washington
  • 68 whole genomes sampled from outside of Washington
  • Samples within Washington were collected between 2020-02-26 and 2020-03-15

How many are infected in Washington?

plot of chunk Cumulative estimated infections through time

plot of chunk Cumulative estimated infections through time log scale

Figure 1: Estimated cumulative infections through time represented by solid black line (median) and 95% CrI (ribbon). Black points represent reported cases in Washington. The dashed line indicates the date of last sample in Washington in this analysis.

  • Estimated cumulative infections at last sample (2020-03-15): 12726 [3899-71563] median [95%CI]

  • Cumulative confirmed infections reported at 2020-03-15: 3745

plot of chunk daily estimated infections through time

plot of chunk daily estimated infections through time log scale

Figure 2: Estimated daily infections through time represented by solid black line (median) and 95% CrI (ribbon). Black points represent reported cases in Washington. The dashed line indicates the date of last sample in Washington in this analysis.

plot of chunk reporting

Figure 3: Estimated percentage of daily cases reported in Washington. Error bars represent the 95% credible interval.

plot of chunk Rt

*Figure 4: Reproduction number through time. The black vertical dashed line indicates the date of last sample in Washington in this analysis. Orange and red dashed lines indicate dates of school closure and general lockdown in Washington, respectively. *

Reproduction number at last sample (2020-03-26): 2.5 [0.94-3.02] median [95% CrI]

How quickly has the epidemic in Washington grown?

Quantile Reproduction number Growth rate (per day) Doubling time (days)
50% 2.71 0.164 4.24
2.5% 2.27 0.128 3.33
97.5% 3.31 0.208 5.42

Table 1: Reproduction number, growth rate and doubling times

How has SARS-CoV 2 evolved in Washington?

plot of chunk mcc_tree

Figure 4: Time scaled phylogeny co-estimated with epidemiological parameters. The colour of the tips corresponds to location sampling; red tips were sampled from within Washington, blue tips from outside.

Molecular clock rate of evolution: 0.00167 [0.00119-0.00247] median [95% CrI]

Methods summary

Details on methods and priors can be found here.

Model version: seijr0.0.0

Report version: 20200420-230114-2d0c42b0

Estimates are based on 10 chains with 20 million iterations and 50% burn-in. Effective sample size values

Acknowledgements

This work was supported by the MRC Centre for Global Infectious Disease Analysis at Imperial College London.

Sequence data were provided by GISAID and these laboratories.